I don’t know the specifics of this project, but not all Amtrak trains are electric, they also run diesel and dual mode (diesel/electric) trains (I’m pretty sure, but not certain that the northeast corridor is all electric)

There’s also other things worth considering like emissions from construction or maintenance vehicles, some lines are used for freight and passenger rail, construction might stir up any crap that might be in the soil, I suspect there’s some amount of metal dust created by the constant grinding of wheels on rails, plastics from brakes and such, leaks from any hydraulics onboard the train, refrigerant leaking from the air conditioning, etc.

In the grand scheme, even if they’re running straight diesel trains, leaking fluids, asbestos brake pads, etc. it’s probably all negligible in emissions compared to just living in Baltimore, maybe even offset if it leads to more people using Amtrak instead of driving but all of it is still worth considering.